X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.2
Temperature 277.0
Details 22% PEG2000MME, 0.2M Ammonium Sulfate, 10mM Cd Sulfate, 1mM NMP, 0.1M sodium acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.27 α = 90
b = 76.24 β = 93.33
c = 60.44 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 -- SSRL BL11-1

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.8 19.79 -- -- -- -- -- 44580 44580 0.0 -3.0 23.8

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.8 19.79 -- 2.0 46434 44164 1341 95.1 -- -- 0.22 0.253 random
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.8 1.88 4049 145 3904 0.315 0.304 0.025 69.9
X Ray Diffraction 1.88 1.98 5426 160 5266 0.247 0.242 0.019 93.6
X Ray Diffraction 1.98 2.1 5681 176 5505 0.228 0.227 0.017 98.2
X Ray Diffraction 2.1 2.27 5733 195 5538 0.226 0.228 0.016 98.9
X Ray Diffraction 2.27 2.49 5769 158 5611 0.228 0.229 0.018 99.5
X Ray Diffraction 2.49 2.86 5796 181 5615 0.226 0.228 0.017 99.8
X Ray Diffraction 2.86 3.59 5812 153 5659 0.226 0.231 0.019 99.9
X Ray Diffraction 3.59 19.79 5898 173 5725 0.198 0.196 0.015 99.9
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.79
Anisotropic B[1][1] 1.43
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 4.95
Anisotropic B[2][2] 3.94
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.37
RMS Deviations
Key Refinement Restraint Deviation
x_torsion_impr_deg 0.78
x_torsion_deg 26.7
x_angle_deg 1.3
x_bond_d 0.005
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.22
Luzzati Sigma A (Observed) 0.13
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.26
Luzzati Sigma A (R-Free Set) 0.18
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3261
Nucleic Acid Atoms 0
Heterogen Atoms 43
Solvent Atoms 505

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
EPMR Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
Crystallography & NMR System version: 1.0 refinement